Evolutionary Flexibility of Ribosome Biogenesis in Bacteria

Ribosomes are essential for protein synthesis and require ribosome biogenesis factors for assembly. To uncover the evolutionary diversity of ribosome biogenesis, we analyzed over 30,000 bacterial genomes and revealed that Candidate Phyla Radiation, also known as the phylum Patescibacteria, characterized by reduced genomes and smaller ribosomes, has about half the average number of ribosome biogenesis factors compared with non-Candidate Phyla Radiation bacteria. Notably, key ribosome biogenesis factors such as der, obgE, and rbfA, considered indispensable, are conserved in only around 20%-70% of Candidate Phyla Radiation genomes. Since such repertoires were not observed in reduced genomes of other phyla, Candidate Phyla Radiation presumably diverged early in bacterial evolution. We further confirmed that ribosomal structural changes correlate with reduced ribosome biogenesis factor, evidencing co-evolution between ribosome biogenesis factor and the ribosome. These findings suggest that ribosomal biogenesis is more flexible than recognized, and the small cell and genome sizes of Candidate Phyla Radiation bacteria and their early divergence may influence the unusual repertoires of ribosome biogenesis factors.